#vcf_to_final_vcf --input_file /data/mus/visitors/lg/full/20100703-isec2-highconf-wref.vcf --output_file /data/mus/visitors/lg/final.vcf --indels_file /data/mus/visitors/lg/short_read_sv/all_indels.expanded_by_15.list --repeats_file /data/mus/visitors/lg/ucsc_data/short.simple_repeats.expanded_by_5.data -v 2 -L logs/final_vcf.log
#vcf_to_final_summary                                                                                                                 \ 
#                --input_file /data/mus/visitors/lg/full/20100703-isec2-highconf-wref.vcf                                             \ 
#                --output_file /data/mus/visitors/lg/final.summary.8_classical_strains                                                \ 
#                --indels_file /data/mus/visitors/lg/short_read_sv/all_indels.expanded_by_15.list                                     \ 
#                --repeats_file /data/mus/visitors/lg/uncallable/simple_repeats.expanded_by_5.data                                    \ 
#		-v 2                                                                                                                  \ 
#		-L logs/final_vcf.log                                                                                                 \ 
#                --only_snp_sites -s AKR -s A_J -s BALB -s C3H -s C57BL -s CBA -s DBA -s LP_J                                         
#vcf_to_final_summary                                                                                                                 \ 
#                --input_file /data/mus/visitors/lg/full/20100703-isec2-highconf-wref.vcf                                             \ 
#                --output_file /data/mus/visitors/lg/final.summary.all                                                                \ 
#                --indels_file /data/mus/visitors/lg/short_read_sv/all_indels.expanded_by_15.list                                     \ 
#                --repeats_file /data/mus/visitors/lg/uncallable/simple_repeats.expanded_by_5.data                                    \ 
#		-v 2                                                                                                                  \ 
#		-L logs/final_vcf.log     
#vcf_to_final_summary                                                                                                                  \
#		--input_file /data/mus/visitors/lg/full/20100703-isec2-highconf-wref.vcf                                              \
#		--output_file /data/mus/visitors/lg/final.summary.4_wild_derived_strains                                              \
#		--indels_file /data/mus/visitors/lg/short_read_sv/all_indels.expanded_by_15.list                                      \
#		--repeats_file /data/mus/visitors/lg/uncallable/simple_repeats.expanded_by_5.data                                     \
#	       -v 2                                                                                                                   \
#	       -L logs/final_vcf.log                                                                                                  \
#		--only_snp_sites -s PWK -s CAST -s SPRET -sWSB
vcf_to_final_summary                                                                                                                  \
		--input_file /data/mus/visitors/lg/full/20100703-isec2-highconf-wref.vcf                                              \
		--output_file /data/mus/visitors/lg/final.summary.all_but_wild_derived_strains                                              \
		--indels_file /data/mus/visitors/lg/short_read_sv/all_indels.expanded_by_15.list                                      \
		--repeats_file /data/mus/visitors/lg/uncallable/simple_repeats.expanded_by_5.data                                     \
	       -v 2                                                                                                                   \
	       -L logs/final_vcf.log                                                                                                  \
		--only_snp_sites -s 129P2 -s 129S1 -s 129S5 -s AKR -s A_J -s BALB -s C3H -s C57BL -s CBA -s DBA -s LP_J -s NOD -s NZO

